While this might also be a "power cotonti user" feature and pretty useless to noobies (people with less than 5 seditio sites, which arent really affected by this problem), it might actually be very interesting to skin makers as well. And easier for skinners = more skins.
Basically my idea is to take the same code from plug.inc.php (the skinning/tpl part) and apply it to taking the skin:

1.) if exists take skin file from current skin directory
2.) else if exists take skin file from default

Basically this would allow:

- skin makers to not need to upload the entire tpl set if they only changed a couple of files

- power users to keep certain parts centralized (like registration screen, page edit and add and similar stuff that almost never gets changed- and if they do get changed you want every file with this name changed ASAP) and only change the parts when you'd upload the actual file in the current skin location.